[gmx-users] Editconf error
Jorge Dagnino
jdagnino at gmail.com
Fri May 22 22:07:59 CEST 2015
Here are the complete files.
pdb2gmx input: http://pastebin.com/HBmrR0eF
.gro output: http://paste2.org/ahY6MB99
editconf input: http://paste2.org/9fPp6J02
editconf output: http://paste2.org/v1IsPp6O
Thanks.
2015-05-22 16:21 GMT-03:00 Barnett, James W <jbarnet4 at tulane.edu>:
> It'd be more helpful for troubleshooting your problem if you post the
> entire file in each case, not just parts of them. If it's a large file use
> Pastebin.com or something similar.
>
> --
> James "Wes" Barnett
> Ph.D. Candidate
> Chemical and Biomolecular Engineering
>
> Tulane University
> Boggs Center for Energy and Biotechnology, Room 341-B
> New Orleans, Louisiana 70118
> jbarnet4 at tulane.edu
> LinkedIn
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Jorge
> Dagnino <jdagnino at gmail.com>
> Sent: Friday, May 22, 2015 11:06 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Editconf error
>
> Here are the coordinates from my pdb file:
>
> ATOM 1 N MET G 27 69.331 43.147 76.443 1.00 0.00
> N
> ATOM 2 CA MET G 27 68.996 44.047 75.331 1.00 0.00
> C
> ATOM 3 C MET G 27 67.818 43.550 74.510 1.00 0.00
> C
> ATOM 4 O MET G 27 66.981 44.264 73.969 1.00 0.00
> O
> ATOM 5 CB MET G 27 70.152 44.201 74.325 1.00 0.00
> C
> ATOM 6 CG MET G 27 70.024 45.547 73.614 1.00 0.00
> C
> ATOM 7 SD MET G 27 70.710 46.841 74.678 1.00 0.00
> S
> ATOM 8 CE MET G 27 70.252 48.118 73.481 1.00 0.00
> C
> ATOM 9 N ALA G 28 67.504 42.250 74.523 1.00 0.00
> N
> ATOM 10 CA ALA G 28 66.247 41.666 74.095 1.00 0.00
> C
> ATOM 11 C ALA G 28 64.968 42.391 74.469 1.00 0.00
> C
> ATOM 12 O ALA G 28 64.064 42.543 73.651 1.00 0.00
> O
> ATOM 13 CB ALA G 28 66.323 40.167 74.396 1.00 0.00
> C
> ATOM 14 N GLU G 29 64.839 42.732 75.756 1.00 0.00
> N
> ATOM 15 CA GLU G 29 63.656 43.315 76.334 1.00 0.00
> C
> ATOM 16 C GLU G 29 63.567 44.789 75.955 1.00 0.00
> C
> ATOM 17 O GLU G 29 62.480 45.354 75.850 1.00 0.00
> O
> ATOM 18 CB GLU G 29 63.662 43.143 77.854 1.00 0.00
> C
> ATOM 19 CG GLU G 29 64.822 43.835 78.553 1.00 0.00
> C
> ATOM 20 CD GLU G 29 64.794 43.644 80.055 1.00 0.00
> C
> ATOM 21 OE1 GLU G 29 63.801 44.058 80.689 1.00 0.00
> O
> ATOM 22 OE2 GLU G 29 65.765 43.078 80.601 1.00 0.00
> O1-
>
> And here are the coordinates from the .gro file
>
> Giant Rising Ordinary Mutants for A Clerical Setup
> 16231
> 27MET N 1 6.933 4.315 7.644
> 27MET H1 2 7.011 4.352 7.695
> 27MET H2 3 6.854 4.307 7.705
> 27MET H3 4 6.957 4.224 7.608
> 27MET CA 5 6.900 4.405 7.533
> 27MET HA 6 6.878 4.489 7.582
> 27MET CB 7 7.015 4.420 7.432
> 27MET HB1 8 7.103 4.416 7.481
> 27MET HB2 9 7.011 4.346 7.365
> 27MET CG 10 7.002 4.555 7.361
> 27MET HG1 11 7.052 4.545 7.275
> 27MET HG2 12 6.905 4.567 7.343
> 27MET SD 13 7.071 4.684 7.468
> 27MET CE 14 7.025 4.812 7.348
> 27MET HE1 15 7.053 4.901 7.383
> 27MET HE2 16 7.071 4.794 7.261
> 27MET HE3 17 6.926 4.811 7.334
> 27MET C 18 6.782 4.355 7.451
> 27MET O 19 6.698 4.426 7.397
> 28ALA N 20 6.750 4.225 7.452
> 28ALA H 21 6.820 4.162 7.486
> 28ALA CA 22 6.625 4.167 7.410
> 28ALA HA 23 6.620 4.184 7.311
> 28ALA CB 24 6.632 4.017 7.440
> 28ALA HB1 25 6.547 3.973 7.411
> 28ALA HB2 26 6.709 3.976 7.389
> 28ALA HB3 27 6.646 4.003 7.538
> 28ALA C 28 6.497 4.239 7.447
> 28ALA O 29 6.406 4.254 7.365
> 29GLU N 30 6.484 4.273 7.576
> 29GLU H 31 6.562 4.257 7.636
> 29GLU CA 32 6.366 4.332 7.633
> 29GLU HA 33 6.289 4.281 7.594
> 29GLU CB 34 6.366 4.314 7.785
> 29GLU HB1 35 6.281 4.352 7.822
> 29GLU HB2 36 6.371 4.217 7.806
> 29GLU CG 37 6.482 4.384 7.855
> 29GLU HG1 38 6.568 4.346 7.820
> 29GLU HG2 39 6.478 4.481 7.836
> 29GLU CD 40 6.479 4.364 8.005
> 29GLU OE1 41 6.380 4.406 8.069
> 29GLU OE2 42 6.576 4.308 8.060
> 29GLU C 43 6.357 4.479 7.595
> 29GLU O 44 6.248 4.535 7.585
>
> and this is the output from editconf.
>
> Giant Rising Ordinary Mutants for A Clerical Setup
> 16231
> 27MET N 1 -nan -nan -nan
> 27MET H1 2 -nan -nan -nan
> 27MET H2 3 -nan -nan -nan
> 27MET H3 4 -nan -nan -nan
> 27MET CA 5 -nan -nan -nan
> 27MET HA 6 -nan -nan -nan
> 27MET CB 7 -nan -nan -nan
> 27MET HB1 8 -nan -nan -nan
> 27MET HB2 9 -nan -nan -nan
> 27MET CG 10 -nan -nan -nan
> 27MET HG1 11 -nan -nan -nan
> 27MET HG2 12 -nan -nan -nan
> 27MET SD 13 -nan -nan -nan
> 27MET CE 14 -nan -nan -nan
> 27MET HE1 15 -nan -nan -nan
> 27MET HE2 16 -nan -nan -nan
> 27MET HE3 17 -nan -nan -nan
> 27MET C 18 -nan -nan -nan
> 27MET O 19 -nan -nan -nan
>
> I hope that this helps.
> Thanks
>
>
> 2015-05-20 22:28 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 5/20/15 5:27 PM, Jorge Dagnino wrote:
> >
> >> Dear GMX users.
> >>
> >> Im trying to create my system and When i use pdb2gmx everything seems
> ok.
> >>
> >> gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id
> >>
> >> Including chain 1 in system: 3235 atoms 203 residues
> >> Including chain 2 in system: 2531 atoms 161 residues
> >> Including chain 3 in system: 2546 atoms 161 residues
> >> Including chain 4 in system: 2531 atoms 161 residues
> >> Including chain 5 in system: 2546 atoms 161 residues
> >> Including chain 6 in system: 2842 atoms 169 residues
> >> Now there are 16231 atoms and 1016 residues
> >> Total mass in system 115288.734 a.m.u.
> >> Total charge in system -17.000 e
> >>
> >> Writing coordinate file...
> >>
> >> --------- PLEASE NOTE ------------
> >> You have successfully generated a topology from: trim.pdb.
> >> The OplsaaPBS force field and the spce water model are used.
> >>
> >> Then when i use the editconf command :
> >>
> >> gmx editconf -f trim.gro -bt dodecahedron -o box -c -d 1.0
> >>
> >>
> >> Read 16231 atoms
> >> Volume: 60.3503 nm^3, corresponds to roughly 27100 electrons
> >> No velocities found
> >> system size : 11.777 11.005 6.369 (nm)
> >> diameter : 12.737 (nm)
> >> center : -nan -nan -nan (nm)
> >> box vectors : 4.144 4.582 3.178 (nm)
> >> box angles : 90.00 90.00 90.00 (degrees)
> >> box volume : 60.35 (nm^3)
> >> shift : -nan -nan -nan (nm)
> >> new center : -nan -nan -nan (nm)
> >> new box vectors : 14.737 14.737 14.737 (nm)
> >> new box angles : 60.00 60.00 90.00 (degrees)
> >> new box volume :2262.99 (nm^3)
> >>
> >> and the ouptut file looks like this.
> >>
> >> Giant Rising Ordinary Mutants for A Clerical Setup
> >> 16231
> >> 27MET N 1 -nan -nan -nan
> >> 27MET H1 2 -nan -nan -nan
> >> 27MET H2 3 -nan -nan -nan
> >> 27MET H3 4 -nan -nan -nan
> >> 27MET CA 5 -nan -nan -nan
> >>
> >> I try to make a bigger box manually, also change the box shape and the
> >> distance but i have the same result,
> >> This is my first time with this kind of error, what is wrong? what am i
> >> missing?
> >>
> >
> > Hard to say; I've never seen anything like this. The 'nan' means "not a
> > number" so the coordinates are junk. Are the coordinates in trim.pdb and
> > trim.gro sound?
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
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>
>
>
> --
> JORGE DAGNINO LEONE
> Bioquímico
> Magíster en Bioquímica y Bioinformática
> Estudiante de Doctorado en Ciencias Biológicas.
> Facultad de Ciencias Biológicas
> Laboratorio de Biofísica Molecular
> Universidad de Concepción
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--
JORGE DAGNINO LEONE
Bioquímico
Magíster en Bioquímica y Bioinformática
Estudiante de Doctorado en Ciencias Biológicas.
Facultad de Ciencias Biológicas
Laboratorio de Biofísica Molecular
Universidad de Concepción
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